The Deep Sea Warehouse is the starting point for undersea operations as it creates a building area and allows exchange of goods with ships like a normal Warehouse. To build a deep sea warehouse, load a submarine with building materials and tools and submerge it at an underwater plateau. The 'build warehouse' button will appear once within range, similar to building new depots at an island with a regular ship. When built, the deep sea warehouse also has an above-water station for normal ships.

The Deep Sea Warehouse has three levels. While the second upgrade just requires Building Modules and Tools, the third upgrade also requires Carbon. The third level of the Deep Sea Warehouse has anti-air defenses like the third level of the Depot and Warehouse. At the first level, the Warehouse has 1000 hitpoints and 50 storage, at the second level 2000 hitpoints and 90 storage, and at the third level 3000 hitpoints and 130 storage. Expanding the Deep Sea Warehouse adds additional underwater transports and passive trading slots, much like a normal Warehouse.

The underwater part doesn't change when you upgrade the warehouse, but the above-water part does.